30th July 2009
The focus of this meeting was to finalize the project proposal, now found at Team:BCCS-Bristol/Project. On the modelling side, we delegated GRNs to Petros/Antos, vesicles to Steve, magnetotaxis to Emily and performance/population dynamics to Mattia. Lab work progresses.
3rd July 2009
The project has gained a direction and a lot of work has been done in both modelling and wet-lab aspects. A review of the project and its goals was given to all advisors and views about further work.
We are improving BSim to have a more "real-life" feeling. Current progress includes the shape of bacteria and population dynamics.
16th July 2009
Discussed the progress of the project. We are currently focused on the vesicle formation part of the project although some steps have been taken in trying to develop magnetotaxis ex vivo.
The relevant presentation can be found here.
9th July 2009
Vesicles with a twist...part II
After a week's worth of digging through the literature we have managed to find possible non-toxic candidate proteins that pack within outer membrane vesicles produced by E.coli. Thus we have settled into implementing directed communication and delivery of proteins of interest between different cells/populations. This will possibly form the bigger part of the project and if time permits we will combine this with our magnetotaxis idea.
With respect to modelling we are interested in developing a useful tool for the community and research by possibly expanding the existing BSim software. For further information visit the modelling page of the wiki.
With respect to the lab we will pursuit the building of biobricks that will allow the implementation of proteins of interest into OMVs (outer membrane vesicles) as a first part to the project. Upon the succesful completion of this first task we want to implement some GRN for the control of responses of both production and/or message acceptance.
A copy of the presentation of this meeting can be found here.
2nd July 2009
Vesicles with a twist
We seem to have settled down to the idea that implementing magnetotaxis in vivo in E.coli will be infeasible within the given time-frame. Instead we have decided to move in the direction where we will try implementing the usage of vesicles in our project.
We are still thinking of perhaps implementing magnetotaxis combined with bacteria in an in vitro manner.
26th June 2009
Ollie and Thanasis spent some time this week looking into whether we could use bacteria to detect and report on the state of an organism. It now seems we have now dropped the idea on the grounds it is too similar to projects attempted in previous years (NYMU, KULeuven) and would require licensing. However there was a suggestion that this idea could be taken in the direction of sequence based toggle switches to carry out a (more complicated) decision tree based diagnosis.
Petros prepared some slides on the biological feasibility of engineering E.coli to synthesize magnetosome (Copy of the presentation found here)
Links to the papers cited in the presentation can be found here:
- Magnetosome formation in prokaryotes
- Magnetotactic bacteria and magnetosomes
- A Magnetosome-specific GTPase from the Magnetic Bacterium Magnetospirillum magneticum AMB-1
- A large gene cluster encoding several magnetosome proteins is conserved in different species of magnetotactic bacteria
- The Escherichia coli Cytochrome c Maturation (Ccm) System Does Not Detectably Attach Heme to Single Cysteine Variants of an Apocytochrome c
- Toward Cloning of the Magnetotactic Metagenome: Identification of Magnetosome Island Gene Clusters in Uncultivated Magnetotactic Bacteria from Different Aquatic sediments
- Genetics and cell biology of magnetosome formation in magnetotactic bacteria
- Complete Genome Sequence of the Facultative Anaerobic Magnetotactic Bacterium Magnetospirillum sp. strain AMB-1
Steve and Emily looked into possible applications of magnetotaxis. These papers seem particularly interesting:
- Controlled manipulation and actuation of micro-objects with magnetotactic bacteria
- Towards Autonomous Bacterial Microrobots
- Other publications by Sylvain Martel
18th June 2009
The shortlist was down to 7 projects and 3 of those made it to the next round as voted by the present audience. These are as follows (project title, (votes received)):
- Magnetic Bacteria (10)
- Bacterial Vesicles (6)
- Non-Invasive Reporting/Switches & Sensors (6)
- Genome Updates & version control (5)
- Host/Parasite Symbiosis (3)
- Bacterial Computation
- RNA Editing
Thus the top three were chosen to review the literature further and assess the possibility of carrying each out in 3 months.
11th June 2009
Kick off meeting. Narrowed down ideas from ~15 to 7. See Team:BCCS-Bristol/Brainstorming.
2nd June 2009
Presentation of initial ideas at MCB2009.